Total dissolved and total particulate Hg mass balances were estimated during one hydrological period (July 2001–June 2002) in the Thur River basin, which is heavily polluted by chlor-alkali industrial activity. The seasonal variations of the Hg dynamics in the aquatic environment were assessed using total Hg concentrations in bottom sediment and suspended matter, and total and reactive dissolved Hg concentrations in the water. The impact of the chlor-alkali plant (CAP) remains the largest concern for Hg contamination of this river system. Upstream from the CAP, the Hg partitioning between dissolved and particulate phases was principally controlled by the dissolved fraction due to snow melting during spring high flow, while during low flow, Hg was primarily adsorbed onto particulates. Downstream from the CAP, the Hg partitioning is controlled by the concentration of dissolved organic and inorganic ligands and by the total suspended sediment (TSS) concentrations. Nevertheless, the particulate fluxes were five times higher than the dissolved ones. Most of the total annual flux of Hg supplied by the CAP to the river is transported to the outlet of the catchment (total Hg flux: 70 lg m2 a1). Downstream from the CAP, the bottom sediment, mainly composed of coarse sediment (>63 lm) and depleted in organic matter, has a weak capacity to trap Hg in the river channel and the stock of Hg is low (4 mg m2) showing that the residence time of Hg in this river is short.